From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jun 21 2013 - 03:50:35 CDT
Hello:
May I ask which one of the examples provided with the recent "Using
collective variables to drive molecular
dynamics simulations" by Fiorin-Klein-Henin could help with problems of
blind ligand-protein docking? I am comparing with "Sampling protein motion
and solvent effect during ligand binding" by Parrinello and associates
www.pnas.org/cgi/doi/10.1073/pnas.1112181108, which was based on
well-tempered metadynamics. This means that I am considering whether such
problems of interaction between proteins and ligands can be treated with
NAMD without the PLUMED plugin. It would simplify the life of NAMD users.
Thanks
francesco pietra
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:20 CST